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comparison EBGeneTwoCondTest.xml @ 10:9adf2362f302 draft

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author ning
date Fri, 15 Mar 2013 18:22:45 -0400
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9:c20070b11b55 10:9adf2362f302
1 <tool id="EBGeneTwoCondTest" name="Gene level DE test across two conditions">
2 <description>Runs EBSeq to find DE genes across two conditions</description>
3 <command>R --quiet --slave --file=$GALAXY_ROOT_DIR/tools/EBSeq/EBGeneTwoCondTest.R --args $Gene_Expression $First_Row_Sample_Names $Conditions $Target_FDR $Output $Sorted_Output $Sorted_Output_with_target_FDR $Sizes</command>
4 <inputs>
5 <param name="Gene_Expression" type="data" format="tabular" label="Gene Expression (tab eliminated, please use the unnormalized values)"/>
6 <param name="First_Row_Sample_Names" type="select" format="text">
7 <label>The First Row is Sample Names?</label>
8 <option value="y">Yes</option>
9 <option value="n">No</option>
10 </param>
11 <param name="Conditions" type="text" size="60" value="C1,C2" label="Enter which condition each
12 sample belongs to (seperated by comma, no space please)."
13 help=""/>
14 <param name="Target_FDR" type="text" format="tabular" value="0.05" label="Target FDR"
15 />
16 </inputs>
17 <outputs>
18 <data format="tabular" name="Output" />
19 <data format="tabular" name="Sorted_Output" />
20 <data format="tabular" name="Sorted_Output_with_target_FDR" />
21 <data format="tabular" name="Sizes" />
22 </outputs>
23
24 <help>
25 The input Conditions should have exactly two levels. The length of the Condition vector should be exactly the same as the number of
26 columns in the data file (except the gene names column).
27
28 Four output files will be generated. Each file contains Posterior probability of being
29 DE (PPDE), Fold Change (RealFC), Posterior Fold Change (PostFC) and normalized gene expressions.
30 The Four files are:
31 Genes with the same order as in input file;
32 Genes sorted by PPDE; DE Genes under target FDR (PPDE>=TargetFDR)
33 and sorted by PPDE.
34 Library size factor for each sample.
35
36 </help>
37
38
39 </tool>